[AMBER] How to assign initial velocities (directly not by increasing temeperature) to water molecules

From: Yan Duan <yduan1.ualberta.ca>
Date: Tue, 30 Jul 2013 15:42:33 -0600

Dear Amber developers and users:
  Hi, I'm a new user of this powerful molecular dynamics software. As I've
asked this problem in the group weeks ago, still I have some questions
regarding the very same issue.
  As I've searched around for days, seems that very few people did this
before: although I know that Amber assign a distribution of velocities
according to the temperature, but what if I'd like to assign specific
velocities directly to the atoms, not by increasing the temperature?

  Many thanks to Jason Swails, http://archive.ambermd.org/201306/0311.html

  I understood that I could do this by modifying the .inpcrd file. But
could you please explain this in some more details? For example, now I did
try to add thousands of lines below the coordinates of atoms in the .inpcrd
file, but how could I let Amber process the modified file? I mean should I
simply add a line of "ntx=5" in the &cntrl and that's it? Or does .inpcrd
file requires a specific format to let Amber read its velocites
information? Since till now my modified .inpcrd file could still not be
accepted by Amber.

  So many thanks for reading this long question and I'm looking forward for
your response!

Many thanks,

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Received on Tue Jul 30 2013 - 15:00:02 PDT
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